I'm not very familiar with the year, and I know you have a lot more electronics to deal with...
but the wires going down to the alt and starter on earlier models from a 14 pin connector (I believe you have a different config.) can have insulation degraded to the point that a short or an open will occur. This can cause a no start or a constant starter engagement. You may have some of this going on (i.e.: if the starter pulse wire connects with a HOT (ALT) wire due to bad insulation this could cause the condition you experience...many people have rewired the harness that goes down some have bought replacements...

Maybe it is just a stuck start relay or something easy...I hope you find out.
Jon